Snakemake report: Include html report in report

user_2082836 0
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I am trying to include in my snakemake report a (sub)report which is an html file in some directory and which includes various images in that same directory. Is there a nice way to do this kind of embedding with the standard snakemake reporting?

With the directive:

output:
    report("reports/somestats.html", category = "someCat")

I manage to get the html file listed under "Results" in the snakemake report.

However, if I click on it, my browser (firefox) asks me what to do with the file and if I tell it to open it with the browser, it opens:

file:///tmp/mozilla_xxx/yyy.html

but the links in the html file, which are relative, are all broken and no image is shown.

I could include all the images directly in the snakemake report but that seems counterproductive as the tool used to generate the html I want to embed has already formatted everything nicely.

snakemake restructuredtext report
1 Answers

A fast'n dirty workaround could be to use os.path.abspath() wherever you refer to your images. This assumes that you have control over the (image)links being created in somestats.html .

user_80134670
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